New & Noteworthy

SGD Help Videos: Working with Lists in YeastMine

July 28, 2015

Understanding lists and knowing how to work with them is crucial to getting the most out of YeastMine. This set of short videos explains everything you need to know.

YeastMine allows you to save objects in lists. Typically, these objects are genes, but you can also make lists of other objects such as Gene Ontology terms or PubMed IDs. One way to create a list in YeastMine is to run a query and save the results in a list. Another way is to type in or upload your own list.

Whenever you create a list in YeastMine, you’re immediately presented with information about the genes in the list, such as Gene Ontology and pathway enrichment, interactions, orthologs, and more. This can help you decide what kind of further analysis you’d like to do.

And what if you create a list but then realize that you forgot to include a gene? No worries. It’s easy to edit your saved lists.

Once you have a list of genes, you can feed it into any template query whose name begins with “Gene” to get results for all of the genes in the list. This powerful feature lets you run successive queries to narrow down your results. For example, you could make a list of all the proteins in a given size range, then query that list to see which ones are located in the nucleus, and finally ask how many of these nuclear proteins have human homologs.

And finally, once you’ve created and saved lists you can do a lot of different things with them: combine them, find their intersection, find genes that are not shared between two lists, or find genes that are in one list but not another. This provides a powerful way to combine or compare results from different YeastMine queries.

As always, please contact us if you have any questions about YeastMine. We’re happy to help!